Publications

Publications from the lab

Trachsel-Moncho L, Mathai BJ, Veroni C, Simonsen A. SNX10 at the crossroad of endocytosis and piecemeal mitophagy. Autophagy. 2025 Sep;21(9):2077-2079. PMID: 40327657
Trachsel-Moncho L, Veroni C, Mathai BJ, Lapao A, Singh S, Asp NT, Schultz SW, Pankiv S, Simonsen A. SNX10 functions as a modulator of piecemeal mitophagy and mitochondrial bioenergetics. J Cell Biol. 2025 May 5;224(5):e202404009. Epub 2025 Mar 7. PMID: 40052924.
Pankiv S, Dahl AK, Aas A, Andersen RL, Brech A, Holland P, Singh S, Bindesbøll C, Simonsen A. BEACH domain proteins function as cargo-sorting adaptors in secretory and endocytic pathways. J Cell Biol. 2024 Dec 2;223(12):e202408173. PMID: 39514288.
Lapao A*, Johnson LS*, Trachsel-Moncho L, Singh S, Ng MYW, Nakken S, Eskelinen EL, Simonsen A. The RAB27A effector SYTL5 regulates mitophagy and mitochondrial metabolism. eLife, 2025
Kaur N, de la Ballina LR, Haukaas HS, Torgersen ML, Radulovic M, Munson MJ, Sabirsh A, Stenmark H, Simonsen A, Carlsson SR, Lystad AH. TECPR1 is activated by damage-induced sphingomyelin exposure to mediate noncanonical autophagy. EMBO J. 2023 Jul 6:e113105. PMID: 37409525.
Ganley IG, Simonsen A. Diversity of mitophagy pathways at a glance. J Cell Sci. 2022 Dec 1; 135(23):jcs259748. PMID: 36504076.
Charsou C, Ng MYW, Simonsen A. Regulation of autophagosome biogenesis and mitochondrial bioenergetics by the cholesterol transport protein GRAMD1C. Autophagy. 2022 Dec 12:1-3. PMID: 36469687.
Ng MYW, Charsou C, Lapao A, Singh S, Trachsel-Moncho L, Schultz SW, Nakken S, Munson MJ, Simonsen A. The cholesterol transport protein GRAMD1C regulates autophagy initiation and mitochondrial bioenergetics. Nat Commun. 2022 Oct 21;13(1):6283. PMID: 36270994.
- Related “Behind the paper” blog at Nature Portfolio Communities, https://cancercommunity.nature.com/posts/gramd1c-mediated-cholesterol-transport-regulates-autophagosome-biogenesis-and-mitochondrial-bioenergetics
Simonsen A, Wollert T. Don't forget to be picky - selective autophagy of protein aggregates in neurodegenerative diseases. Curr Opin Cell Biol. 2022 Apr;75:102064. PMID: 35240373.
Reggiori F, Boya P, da Costa D, Elazar Z, Eskelinen EL, Farrés J, Guettler S, Kraft C, Jungbluth H, Martinez A, Morel E, Pless O, Proikas-Cezanne T, Simonsen A. The mechanism of macroautophagy: The movie. Autophagy Rep. 2022 Sep 14;1(1):414-417. PMID: 38106995
Søreng K, Pankiv S, Bergsmark C, Haugsten EM, Dahl AK, de la Ballina LR, Yamamoto A, Lystad AH, Simonsen A. ALFY localizes to early endosomes and cellular protrusions to facilitate directional cell migration. J Cell Sci. 2022 Feb 15;135(4):jcs259138. PMID: 35099014.
Munson MJ, Mathai BJ, Ng MYW, Trachsel-Moncho L, de la Ballina LR, Simonsen A. GAK and PRKCD kinases regulate basal mitophagy. Autophagy. 2022 Jan 9: 1-3.
Kulbhushan Sharma, Nagham T. Asp, Sean Harrison, Richard Siller, Saphira F. Baumgarten, Swapnil Gupta, Maria E Chollet, Elisabeth Andersen, Gareth J. Sullivan, Anne Simonsen. Autophagy modulates cell fate decisions during lineage commitment. Autophagy. 20 Nov 21; 1-17.
Michael J. Munson, Benan J. Mathai, Matthew Yoke Wui Ng, Laura Trachsel-Moncho, Laura de la Ballina, Sebastian W. Schultz, Yahyah Aman, Alf H. Lystad, Sakshi Singh, Sachin Singh, Jørgen Wesche, Evandro F. Fang, Anne Simonsen. GAK and PRKCD are positive regulators of PRKN-independent mitophagy. Nature Communications. 2021 Oct 20; 12 (1): 6101.
Matthew Yoke Wui Ng, Timothy Wai, Anne Simonsen. Quality control of the mitochondrion. Developmental Cell. 2021 April 5; 56 (7): 881-905.
Petra Terešak, Ana Lapao, Nemanja Subic, Patricia Boya, Zvulun Elazar, Anne Simonsen. Regulation of PRKN-independent mitophagy. Autophagy. 20 Feb 25; 1-16.
Melia TJ, Lystad AH, Simonsen A. Autophagosome biogenesis: From membrane growth to closure. J Cell Biol. 2020 Jun 1; 219 (6): e202002085.
Bindesbøll C, Aas A, Ogmundsdottir MH, Pankiv S, Reine T, Zoncu R, Simonsen A. NBEAL1 controls SREBP2 processing and cholesterol metabolism and is a susceptibility locus for coronary artery disease. Sci Rep. 2020 Mar 11; 10 (1): 4528.
Herhaus L, Bhaskara RM, Lystad AH, Gestal-Mato U, Covarrubias-Pinto A, Bonn F, Simonsen A, Hummer G, Dikic I. TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Rep. 2020 Jan 7; 21 (1): e48317.
Herzog LK, Kevei É, Marchante R, Böttcher C, Bindesbøll C, Lystad AH, Pfeiffer A, Gierisch ME, Salomons FA, Simonsen A, Hoppe T, Dantuma NP. The Machado-Joseph disease deubiquitylase ataxin-3 interacts with LC3C / GABARAP and promotes autophagy. Aging Cell. 2020 Jan; 19 (1): e13051.
de la Ballina LR, Munson MJ, Simonsen A. Lipids and Lipid-Binding Proteins in Selective Autophagy. J Mol Biol. 2020 Jan 3; 432 (1): 135-159.
Princely Abudu Y, Pankiv S, Mathai BJ, Håkon Lystad A, Bindesbøll C, Brenne HB, Yoke Wui Ng M, Thiede B, Yamamoto A, Mutugi Nthiga T, Lamark T, Esguerra CV, Johansen T, Simonsen A. NIPSNAP1 and NIPSNAP2 Act as "Eat Me" Signals for Mitophagy. Dev Cell. 2019 May 20; 49 (4): 509-525.e12.
Lystad AH, Carlsson SR, de la Ballina LR, Kauffman KJ, Nag S, Yoshimori T, Melia TJ, Simonsen A. Distinct functions of ATG16L1 isoforms in membrane binding and LC3B lipidation in autophagy-related processes. Nat Cell Biol. 2019 Mar; 21 (3): 372-383.
Simonsen A. Confidence to go the way science takes you. Nat Cell Biol. 2018 Sep; 20 (9): 1009.
Søreng K, Munson MJ, Lamb CA, Bjørndal GT, Pankiv S, Carlsson SR, Tooze SA, Simonsen A. SNX18 regulates ATG9A trafficking from recycling endosomes by recruiting Dynamin-2. EMBO Rep. 2018 Apr; 19 (4). pii: e44837.
Søreng K, Neufeld TP, Simonsen A. Membrane Trafficking in Autophagy. Int Rev Cell Mol Biol. 2018; 336: 1-92.
Mathai BJ, Meijer AH, Simonsen A. Studying Autophagy in Zebrafish. Cells. 2017 Jul 9; 6 (3). pii: E21.
Søreng K, Knævelsrud H, Holland P, Simonsen A. HS1BP3 inhibits autophagy by regulation of PLD1. Autophagy. 2017 May 4; 13 (5): 985-986.
Aas A, Isakson P, Bindesbøll C, Alemu EA, Klungland A, Simonsen A. Nucleocytoplasmic Shuttling of FTO Does Not Affect Starvation-Induced Autophagy. PLoS One. 2017 Mar 13; 12 (3): e0168182.
Holland P, Knævelsrud H, Søreng K, Mathai BJ, Lystad AH, Pankiv S, Bjørndal GT, Schultz SW, Lobert VH, Chan RB, Zhou B, Liestøl K, Carlsson SR, Melia TJ, Di Paolo G, Simonsen A. HS1BP3 negatively regulates autophagy by modulation of phosphatidic acid levels. Nat Commun. 2016 Dec 22; 7: 13889.
Simonsen A. [Self-devouring prolongs life]. Tidsskr Nor Laegeforen. 2016 Dec 6; 136 (22): 1873.
Shatz O, Holland P, Elazar Z, Simonsen A. Complex Relations Between Phospholipids, Autophagy, and Neutral Lipids. Trends Biochem Sci. 2016 Nov; 41 (11): 907-923. Review.
Dragich JM, Kuwajima T, Hirose-Ikeda M, Yoon MS, Eenjes E, Bosco JR, Fox LM, Lystad AH, Oo TF, Yarygina O, Mita T, Waguri S, Ichimura Y, Komatsu M, Simonsen A, Burke RE, Mason CA, Yamamoto A. Autophagy linked FYVE (Alfy / WDFY3) is required for establishing neuronal connectivity in the mammalian brain. Elife. 2016 Sep 20; 5. pii: e14810.
Lystad AH, Simonsen A. Phosphoinositide-binding proteins in autophagy. FEBS Easy. 2016 Aug; 590 (15): 2454-68. Review.
Ylä-Anttila P, Mikkonen E, Happonen KE, Holland P, Ueno T, Simonsen A, Eskelinen EL. RAB24 facilitates clearance of autophagic compartments during basal conditions. Autophagy. 2015; 11 (10): 1833-48.
Holland P and Simonsen A. Actin shapes the autophagosome. Nat Cell Biol. 2015 Sep; 17 (9): 1094-6.
Carlsson SR, Simonsen A. Membrane dynamics in autophagosome biogenesis. J Cell Sci. 2015 15; 128 (2): 193-205. Review
Lystad AH, Simonsen A. Assays to monitor aggrephagy. Methods. 2015 Mar; 75: 112-9.
Holland P, Torgersen ML, Sandvig K, Simonsen A. LYST affects lysosome size and quantity, but not trafficking or degradation through autophagy or endocytosis. Traffic. 2014 Dec; 15 (12): 1390-405.
Lystad AH, Ichimura Y, Takagi K, Yang Y, Pankiv S, Kanegae Y, Kageyama S, Suzuki M, Saito I, Mizushima T, Komatsu M, Simonsen A. Structural determinants in GABARAP required for the selective binding and recruitment of ALFY to LC3B-positive structures. EMBO Rep. 2014 May; 15 (5): 557-65.
Torgersen ML, Simonsen A. Autophagy: friend or foe in the treatment of fusion protein-associated leukemias? Autophagy. 2013 Dec; 9 (12): 2175-7.
Isakson P, Lystad AH, Breen K, Koster G, Stenmark H, Simonsen A. TRAF6 mediates ubiquitination of KIF23 / MKLP1 and is required for midbody ring degradation by selective autophagy. Autophagy. 2013 Dec; 9 (12): 1955-64.
Knaevelsrud H, Carlsson SR, Simonsen A. SNX18 tubulates recycling endosomes for autophagosome biogenesis. Autophagy. 2013 Oct; 9 (10): 1639-41.
Torgersen ML, Engedal N, Boe SO, Hokland P, Simonsen A. Targeting autophagy potentiates the apoptotic effect of histone deacetylase inhibitors in t (8; 21) AML cells. Blood. 2013 Oct 3; 122 (14): 2467-76.
Knaevelsrud H, Soreng K, Raiborg C, Haberg K, Rasmuson F, Brech A, Liestol K, Rusten TE, Stenmark H, Neufeld TP, Carlsson SR, Simonsen A. Membrane remodeling by the PX-BAR protein SNX18 promotes autophagosome formation. J Cell Biol. 2013 Jul 22; 202 (2): 331-49.
Isakson P, Holland P and Simonsen A. The role of ALFY in selective autophagy. Cell Death Differ. 2013 Jan; 20 (1): 12-20.
Reggiori F, Komatsu M, Finley K, Simonsen A. Autophagy: more than a nonselective pathway. Int J Cell Biol. 2012; 2012: 219625.
Knævelsrud H and Simonsen A. Lipids in autophagy: constituents, signaling molecules and cargo with relevance to disease. Biochim Biophys Acta. 2012 Aug; 1821 (8): 1133-45. Review
Bartlett BJ, Isakson P, Lewerenz J, Sanchez H, Kotzebue RW, Cumming RC, Harris GL, Neziz IP, Schubert DR, Simonsen A and Finley KD. p62, Ref (2) P and ubiquitinated proteins are conserved markers of neuronal aging, aggregate formation and progressive autophagic defects. Autophagy. 2011 Jun; 7 (6): 572-83.
Yamamoto A and Simonsen A. The elimination of accumulated and aggregated proteins: a role for aggrephagy in neurodegeneration. Neurobiol Dis. 2011 Jul; 43 (1): 17-28. Review
Knævelsrud H, Ahlquist T, Stenmark H, Merok MA, Nesbakken A, Lothe RA and Simonsen A. UVRAG mutations associated with microsatellite unstable colon cancer do not affect autophagy. Autophagy. 2010 Oct; 6 (7): 863-70.
Isakson P, Bjørås M, Bøe SO and Simonsen A. Autophagy contributes to therapy-induced degradation of the PML / RARA oncoprotein. Blood. 2010 Sep 30; 116 (13): 2324-31.
Filimonenko M, Isakson P., Finley K., Anderson M., Jeong H, Melia TJ, Bartlett BJ, Myers K., Birkeland HG, Lamark T., Krainc D, Brech H., Stenmark H, Simonsen A *, Yamamoto A *. The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell. 2010 Apr 23; 38 (2): 265-79. * shared corresponding. This paper was commented in DevCell Volume 18, Issue 5, 18 May 2010, Pages 694-696
Knaevelsrud H, Simonsen A. Fighting disease by selective autophagy of aggregate-prone proteins. FEBS Easy. 2010 Jun 18; 584 (12): 2635-45.
Claussen TH, Lamark T., Isakson P., Finley K., Brech A., Øvervatn A., Stenmark H., Bjørkøy G., Simonsen A. * and Johansen T *. p62 / SQSTM1 and ALFY interact to facilitate the formation of p62 bodies / ALIS and their degradation by autophagy. Autophagy. 2010 Apr; 6 (3): 330-44. * shared corresponding.
Simonsen A and Tooze SA. Coordination of membrane events during autophagy by multiple class III PI3-kinase complexes. J Cell Biol. 2009 Sep 21; 186 (6): 773-82.
Nezis IP, Simonsen A., Sagona AP, Finley K., Gaumer S., Contamine D., Rusten TE, Stenmark H. and Brech A. Ref (2) P, the Drosophila melanogaster homologue of mammalian p62, is required for the formation of protein aggregates in adult brain. J Cell Biol. 2008 Mar 24; 180 (6): 1065-71.
Simonsen A., Cumming RC., Brech A., Isakson P., Schubert D. and Finley KD Promoting basal levels of autophagy in the nervous system enhances longevity and oxidant resistance in adult Drosophila. Autophagy. 2008 Feb; 4 (2): 176-84. This paper got the cover picture of the same issue of Autophagy and was commented in 'Editors' choice', Science (2007), 318: 1697
Filimonenko M., Stuffers S., Raiborg C., Yamamoto A., Malerød L., Fisher EM, Isaacs A., Brech A., Stenmark H. and Simonsen A. Functional multivesicular bodies are required for autophagic clearance of protein aggregates associated with neurodegenerative disease. J Cell Biol. 2007 Nov 5; 179 (3): 485-500. This paper was commented in 'In this issue', J.Cell Biol., 179 (3): 360 and got the cover picture of the same issue.
Simonsen A., Cumming RC., Lindmo K., Galavis V., Cheng S., Rusten TE. and Finley KD Genetic modifiers of the Drosophila blue cheese gene link defects in lysosomal transport with decreased life span and altered ubiquitinated-protein profiles. Genetics. 2007 Jun; 176 (2): 1283-97.
Simonsen, A., Birkeland, HC, Gillooly, D., Mizushima, N., Kuma, A., Yoshimori, T., Slagsvold, T., Brech, A., and Stenmark, H. Alfy, a novel FYVE- domain-containing protein associated with protein granules and autophagic membranes. J Cell Sci. 2004 Aug 15; 117 (Pt 18): 4239-51.
Simonsen, A, Lippé, R, Christoforidis, S, Gaullier, JM, Brech A, Callaghan, J, Toh, BH, Murphy, C; Zerial, M and Stenmark, H. EEA1 links PI (3) K function to Rab5 regulation of endosome fusion. Nature. 1998 Jul 30; 394 (6692): 494-8. This paper was commented in 'News and Views', Nature , 394 (6692), 426-427

Published June 17, 2022 11:18 AM - Last modified Nov. 11, 2025 8:23 AM